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Wageningen University and Research Centre

EducationWageningen, Netherlands
About: Wageningen University and Research Centre is a education organization based out in Wageningen, Netherlands. It is known for research contribution in the topics: Population & Sustainability. The organization has 23474 authors who have published 54833 publications receiving 2608897 citations.


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Journal ArticleDOI
22 Nov 2007-Nature
TL;DR: It is experimentally demonstrated that a change in conformation of LHCII occurs in vivo, which opens a channel for energy dissipation by transfer to a bound carotenoid, suggesting that this is the principal mechanism of photoprotection.
Abstract: Under conditions of excess sunlight the efficient light-harvesting antenna found in the chloroplast membranes of plants is rapidly and reversibly switched into a photoprotected quenched state in which potentially harmful absorbed energy is dissipated as heat, a process measured as the non-photochemical quenching of chlorophyll fluorescence or qE. Although the biological significance of qE is established, the molecular mechanisms involved are not. LHCII, the main light-harvesting complex, has an inbuilt capability to undergo transformation into a dissipative state by conformational change and it was suggested that this provides a molecular basis for qE, but it is not known if such events occur in vivo or how energy is dissipated in this state. The transition into the dissipative state is associated with a twist in the configuration of the LHCII-bound carotenoid neoxanthin, identified using resonance Raman spectroscopy. Applying this technique to study isolated chloroplasts and whole leaves, we show here that the same change in neoxanthin configuration occurs in vivo, to an extent consistent with the magnitude of energy dissipation. Femtosecond transient absorption spectroscopy, performed on purified LHCII in the dissipative state, shows that energy is transferred from chlorophyll a to a low-lying carotenoid excited state, identified as one of the two luteins (lutein 1) in LHCII. Hence, it is experimentally demonstrated that a change in conformation of LHCII occurs in vivo, which opens a channel for energy dissipation by transfer to a bound carotenoid. We suggest that this is the principal mechanism of photoprotection.

815 citations

Journal ArticleDOI
TL;DR: HOPE is described, a fully automatic program that analyzes the structural and functional effects of point mutations and builds a report with text, figures, and animations that is easy to use and understandable for (bio)medical researchers.
Abstract: Background: Many newly detected point mutations are located in protein-coding regions of the human genome. Knowledge of their effects on the protein’s 3D structure provides insight into the protein’s mechanism, can aid the design of further experiments, and eventually can lead to the development of new medicines and diagnostic tools. Results: In this article we describe HOPE, a fully automatic program that analyzes the structural and functional effects of point mutations. HOPE collects information from a wide range of information sources including calculations on the 3D coordinates of the protein by using WHAT IF Web services, sequence annotations from the UniProt database, and predictions by DAS services. Homology models are built with YASARA. Data is stored in a database and used in a decision scheme to identify the effects of a mutation on the protein’s 3D structure and function. HOPE builds a report with text, figures, and animations that is easy to use and understandable for (bio) medical researchers. Conclusions: We tested HOPE by comparing its output to the results of manually performed projects. In all straightforward cases HOPE performed similar to a trained bioinformatician. The use of 3D structures helps optimize the results in terms of reliability and details. HOPE’s results are easy to understand and are presented in a way that is attractive for researchers without an extensive bioinformatics background. Background The omics-revolution has led to a rapid increase in detected disease-related human mutations. A considerable fraction of these mutations is located in proteincoding regions of the genome and thus can affect the structure and function of that protein, thereby causing a phenotypic effect. Knowledge of these structural and functional effects can aid the design of further experiments and can eventually lead to the development of better disease diagnostics or even medicines to help cure patients. The analysis of mutations that cause the EEC syndrome, for example, revealed that some patients carry a mutation that disturbs dimerisation of the affected P63 protein [1]. This information has triggered a search for drugs http://www.epistem.eu; [2]). In another case, the study of a mutation in the human hemochromatosis protein (HFE), which causes hereditary hemochromatosis, resulted in new insights that are now being used to develop novel diagnostic methods [3]. These and numerous other examples have highlighted the importance of using heterogeneous data, especially structure information, in the study of human disease-linked protein variants. The data that can aid our understanding of the underlying mechanism of disease related mutations can range from the protein’s three-dimensional (3D) structure to its role in biological pathways, or from information generated by mutagenesis experiments to predicted functional motifs. Collecting all available information related to the protein of interest can be challenging and timeconsuming. It is a difficult task to extract exactly those pieces of information that can lead to a conclusion about the effects of a mutation. Several online Web servers exist that offer help to the (bio)medical researcher in predicting these effects. These servers use information from a wide range of sources to reach conclusions

812 citations

Journal ArticleDOI
TL;DR: The expression pattern of BABY BOOM in developing seeds combined with the BBM overexpression phenotype suggests a role for this gene in promoting cell proliferation and morphogenesis during embryogenesis.
Abstract: The molecular mechanisms underlying the initiation and maintenance of the embryonic pathway in plants are largely unknown. To obtain more insight into these processes, we used subtractive hybridization to identify genes that are upregulated during the in vitro induction of embryo development from immature pollen grains of Brassica napus (microspore embryogenesis). One of the genes identified, BABY BOOM (BBM), shows similarity to the AP2/ERF family of transcription factors and is expressed preferentially in developing embryos and seeds. Ectopic expression of BBM in Arabidopsis and Brassica led to the spontaneous formation of somatic embryos and cotyledon-like structures on seedlings. Ectopic BBM expression induced additional pleiotropic phenotypes, including neoplastic growth, hormone-free regeneration of explants, and alterations in leaf and flower morphology. The expression pattern of BBM in developing seeds combined with the BBM overexpression phenotype suggests a role for this gene in promoting cell proliferation and morphogenesis during embryogenesis.

811 citations

Journal ArticleDOI
TL;DR: Polystyrene microplastic had statistically significant effects on the organisms' fitness and bioaccumulation, but the magnitude of the effects was not high, and may be different for sites with different plastic concentrations, or plastics with a higher affinity for POPs.
Abstract: It has been speculated that marine microplastics may cause negative effects on benthic marine organisms and increase bioaccumulation of persistent organic pollutants (POPs). Here, we provide the first controlled study of plastic effects on benthic organisms including transfer of POPs. The effects of polystyrene (PS) microplastic on survival, activity, and bodyweight, as well as the transfer of 19 polychlorinated biphenyls (PCBs), were assessed in bioassays with Arenicola marina (L.). PS was pre-equilibrated in natively contaminated sediment. A positive relation was observed between microplastic concentration in the sediment and both uptake of plastic particles and weight loss by A. marina. Furthermore, a reduction in feeding activity was observed at a PS dose of 7.4% dry weight. A low PS dose of 0.074% increased bioaccumulation of PCBs by a factor of 1.1–3.6, an effect that was significant for ΣPCBs and several individual congeners. At higher doses, bioaccumulation decreased compared to the low dose, whic...

811 citations

Journal ArticleDOI
TL;DR: Even though glucosinolates are constitutive defenses, their levels are influenced by abiotic and biotic factors including insect damage.
Abstract: Glucosinolates present classical examples of plant compounds affecting insect-plant interactions. They are found mainly in the family Brassicaceae, which includes several important crops. More than 120 different glucosinolates are known. The enzyme myrosinase, which is stored in specialized plant cells, converts glucosinolates to the toxic isothiocyanates. Insect herbivores may reduce the toxicity of glucosinolates and their products by excretion, detoxification, or behavioral adaptations. Glucosinolates also affect higher trophic levels, via reduced host or prey quality or because specialist herbivores may sequester glucosinolates for their own defense. There is substantial quantitative and qualitative variation between plant genotypes, tissues, and ontogenetic stages, which poses specific challenges to insect herbivores. Even though glucosinolates are constitutive defenses, their levels are influenced by abiotic and biotic factors including insect damage. Plant breeders may use knowledge on glucosinolates to increase insect resistance in Brassica crops. State-of-the-art techniques, such as mutant analysis and metabolomics, are necessary to identify the exact role of glucosinolates.

810 citations


Authors

Showing all 23851 results

NameH-indexPapersCitations
Walter C. Willett3342399413322
Albert Hofman2672530321405
Frank B. Hu2501675253464
Willem M. de Vos14867088146
Willy Verstraete13992076659
Jonathan D. G. Jones12941780908
Bert Brunekreef12480681938
Pedro W. Crous11580951925
Marten Scheffer11135073789
Wim E. Hennink11060049940
Daan Kromhout10845355551
Peter H. Verburg10746434254
Marcel Dicke10761342959
Vincent W. V. Jaddoe106100844269
Hao Wu10566942607
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
2023278
2022861
20214,144
20203,722
20193,443
20183,226